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PDF management and fixes in EndNote

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How to attach or import PDF files to your library

You can attach or import PDF articles to your EndNote library in five ways:

  1. Select a reference and then choose EndNote: References > File attachements > Attach file.
  2. Select a reference and then click the Paper clip button (Reference panel top-right).
  3. Drag and drop a PDF file onto a reference in your library.
  4. Import PDFs by choosing EndNote: File > Import > File (remember to set Import Option = PDF) or Folder (note check option for also importing sub-folders)
  5. When a PDF is added to your library EndNote saves a copy of the file in the PDF folder inside your library .DATA folder. Then EndNote creates a (relative) link to the copied PDF. This means that you can delete the original file.
  6. Create a new reference (EndNote: References > New Reference), and enter the DOI number into the DOI field. Close (and save) the new reference. Right-click the reference and:
    1. Choose Find Full Text > Find Full Text) to find and attach the PDF (must be free/open).
    2. Choose Find Reference Updates to find and update reference data.

About the library PDF folder

An EndNote library consist of a library file (YourLibraryName.enl) and a corresponding data folder (YourLibraryName.DATA). Both must be in the same folder on your computer, and both must have the exact same name.

If you attach a file to a reference in your library, EndNote will create a PDF folder inside your data folder. You can navigate to this folder to check the content. If you are unsure where your EndNote library is saved on your computer please open your library and choose EndNote: Tools > Library Summary. The location/path to your EndNote library is given in the Location field. The corresponding data folder is in same folder as this location/path.

All your PDFs are saved in separate subfolders inside your PDF folder (inside your library .DATA folder). This makes it hard to get an overview. To list all the PDFs contained in the PDF folder you can do a search for .pdf in your PDF folder, and the search result will list all PDFs. This way you can sort them by i.e. size to see if there are any PDF files with abnormal size (20 MB+) that could cause problems/slowness/corruption to your library.

PDF Handling

You can chose how EndNote does the automatic (or none) renaming of your PDF files by going here: EndNote: Edit > Preferences > PDF Handling.

Here you can also choose a folder on your computer for automatic import. This way every time you open your library EndNote will check this folder. If EndNote finds a new PDF file it will import and add it to your library automatically. This way you can put PDF files you want to keep into this folder and EndNote will take care of the rest.

How to rename existing PDF files in your library

  1. Open your library.
  2. Choose EndNote: Edit > Preferences > PDF Handling.
  3. Choose your preferred naming of your PDF files, i.e. Author-Year or something else which suit your needs. This is to avoid that the PDF attachments get too long names (> 255 characters) or strange names e.g. like '13-%2056&$@8C%29_F%28T%29_PF1%28PRP%29_PFA%.pdf'.
  4. Click OK.
  5. Select all references in your library (EndNote: Edit > Select all, or click one reference in your library and type Ctrl+A).
  6. Choose EndNote: References > File Attachments > Rename PDFs.
  7. Choose for example Author-Year (or something else which suit your needs), and then click OK.

How to find and fix broken attachment links in your library

  1. Select all references once again (EndNote: Edit > Select all, or click one reference in your library and type Ctrl+A)
  2. Choose EndNote: Tools > Find Broken Attachment Links
  3. Remove the 'orphan' (PDF or other type) attachments and add the right attachment(s).
  4. Check the content of the Trash and empty the Trash.
  5. Alternatively, do the following EndNote: References > File Attachments > Convert to Relative Links. This will make sure the PDFs are stored in the subfolder PDF in the .Data folder of the library.

Tips: If you have many broken-PDF-link references in your libary, you can select all references in your library (Ctrl+A), then copy them (Ctrl+C), then create a new library and paste all references into the new library (Ctrl+V), and all broken-PDF-links messages will be gone.

How to add full and abbreviated Journal names to your library

  1. Choose EndNote: Tools > Define Term Lists, then choose Journals and click the Import List button. The default folder for Journal Name lists/files are usually located here on your computer: c:programs (x86)\endnote\Terms Lists.
  2. Import the right Journal Name list for your research area (i.e. Medical): Long names, Short names, Short names with periods and Custom names. This will avoid wrong entry and import of the Journal Name names.
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